It's not a glitch, just a consequence. The box you saw in the original Fixedsys (along with any euro sign, bullet, or TM sign) was actually not part of Fixedsys. That was your OS substituting. If you feel it important, I can place box glyphs at the control code codepoints in the main 256, but I'm not going to put rectangles at every (so far) unused codepoint available
Let me know if I should add them.